1HP1

5'-NUCLEOTIDASE (OPEN FORM) COMPLEX WITH ATP

Summary for 1HP1

• Entry DOI: 10.2210/pdb1hp1/pdb
• Related: 1HO5 1HPU 1USH 2USH
• Descriptor: 5'-NUCLEOTIDASE, ZINC ION, CARBONATE ION, ... (6 entities in total)
• Functional Keywords: metallophosphatase, dinuclear, metalloenzyme, hydrolase, domain movement
• Biological source: Escherichia coli
• Cellular location: Periplasm: P07024
• Total number of polymer chains: 1
• Total formula weight: 58230.71

Authors

Knoefel, T.,Straeter, N. (deposition date: 2000-12-12, release date: 2002-03-20, Last modification date: 2024-11-06)

Primary citation

Knofel, T.,Strater, N.
Mechanism of hydrolysis of phosphate esters by the dimetal center of 5'-nucleotidase based on crystal structures.
J.Mol.Biol., 309:239-254, 2001

PubMed Abstract: 5'-Nucleotidase belongs to a large superfamily of distantly related dinuclear metallophosphatases including the Ser/Thr protein phosphatases and purple acid phosphatases. The protein undergoes a 96 degrees domain rotation between an open (inactive) and a closed (active) enzyme form. Complex structures of the closed form with the products adenosine and phosphate, and with the substrate analogue inhibitor alpha,beta-methylene ADP, have been determined at 2.1 A and 1.85 A resolution, respectively. In addition, a complex of the open form of 5'-nucleotidase with ATP was analyzed at a resolution of 1.7 A. These structures show that the adenosine group binds to a specific binding pocket of the C-terminal domain. The adenine ring is stacked between Phe429 and Phe498. The N-terminal domain provides the ligands to the dimetal cluster and the conserved His117, which together form the catalytic core structure. However, the three C-terminal arginine residues 375, 379 and 410, which are involved in substrate binding, may also play a role in transition-state stabilization. The beta-phosphate group of the inhibitor is terminally coordinated to the site 2 metal ion. The site 1 metal ion coordinates a water molecule which is in an ideal position for a nucleophilic attack on the phosphorus atom, assuming an in-line mechanism of phosphoryl transfer. Another water molecule bridges the two metal ions.

PubMed: 11491293
DOI: 10.1006/jmbi.2001.4656

Experimental method

X-RAY DIFFRACTION (1.7 Å)